Mercurial > repos > jjohnson > bcftools_convert_to_vcf

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sun, 26 Jun 2016 15:34:05 -0400
parents bca07db8f55c
children
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bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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1 ##fileformat=VCFv4.1
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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2 ##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag">
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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3 ##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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4 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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5 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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6 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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7 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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8 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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9 ##FILTER=<ID=q10,Description="Quality below 10">
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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10 ##FILTER=<ID=test,Description="Testing filter">
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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11 ##contig=<ID=1,assembly=b37,length=249250621>
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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12 ##contig=<ID=2,assembly=b37,length=249250621>
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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13 ##contig=<ID=3,assembly=b37,length=198022430>
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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14 ##contig=<ID=4,assembly=b37,length=191154276>
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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15 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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16 ##readme=AAAAAA
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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17 ##readme=BBBBBB
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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18 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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19 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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20 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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21 ##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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22 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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23 1 3000000 . C G 59.2 PASS AN=4;AC=2 GT:GQ 0/1:245 0/1:245
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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24 1 3000150 . C G 59.2 PASS AN=4;AC=2 GT:GQ 0/1:245 0/1:245
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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25 1 3000151 . C G 59.2 PASS AN=4;AC=2 GT:DP:GQ 0/1:32:245 0/1:32:245
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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26 1 3106154 . C CCC 342 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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27 1 3106154 . C T 59.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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28 1 3200000 . C T 59.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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29 1 3200010 . c A,T 59.2 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32
bca07db8f55c planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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30 1 3200020 . C T,G 59.2 PASS AN=4;AC=2 GT:GL ./.:1,4,6,2,5,3 .:1,3,2